1tdh

=DNA repair protein human endonuclease VIII-like 1 (NEIL1)=

Human Neil1 is a base-excision DNA repair protein which shows preference for repairing oxidation products of 8-oxoguanine. It is part of the base-excision repair system, which consists of families of proteins that protect the genome against endogenous and exogenous damages by repairing damaged DNA.

This structure consists of two domains connected by a hinge polypeptide, with an N-terminal domain consisting of a Beta sandwich with two alpha-helices , and 4 alpha-helices on the C-terminus. Including a H2TH motif. (1tdh)

About this Structure
1TDH is a Single protein structure of sequence from Homo sapiens. Full crystallographic information is available from OCA.

DNA Repair and Base Excision DNA Repair
For a video of DNA repair click here. The picture below also illustrates DNA repair: The genome of any living organisms is being continuously affected by exogenous and endogenous agents, such as ultraviolet light, ionizing radiation, different chemicals and the cell's own metabolites (such as reactive oxygen). Therefore, different systems have evolved to repair these damages. With some of these systems shared throughout all lifeforms. Therefore, the proper functioning of DNA repair is critical for survival. There are six pathways of DNA repair (reviewed in Friedberg et al), and one of the is base-excision repair. The latter's distinguishing feature is that it removes lesions as single bases, as opposed to dNMPs or short oligonucleotides like other systems.

Base excision repair's signature enzyme are the DNA glycosylases. These enzymes work by recognizing and removing a single damaged base from DNA. They are called DNA glycosylases because they hydrolize the N-glycosidic bond of the damaged deoxynucleoside. The subsequent steps of the pathway (strand incision, gap-filling and ligation) are done by other enzymes. See below for a cartoon of the process :

Evolution and related structures
Neil1 is part of the FpgNei superfamily of base excision repair proteins. And its one of 3 DNA glycosylases present in vertebrates, and in humans in particular. The evolution of this superfamily is not totally clear. Homologous structures have been solved, including Fpg protein from Lactococcus Lactis (1pjj), Bacillus Stereothermophilus (1r2y) , Thermos Thermophilus (1ee8) and Escherichia Coli(1k82) and Nei from Escherichia Coli (1k3w). The overall structure is similar, and some of the damages include 8-oxoguanine and fapyG (1xc8).

Population variants can be found in hapmap project.

= Human Neil1 Function=

Role in Base excision repair
Neil1 has as preferred substrate oxidation products of 8-Oxoguanine: spiroiminodihydantoin (Sp) and guanidinohydantoin (Gh). . 8-oxoG produces hight levels of G:C → T:A transversion mutations in mammalian and bacterial cells. In turn, site-specific oxidation of 8-oxoG can lead to the lesions Gh/Ia and Sp, leading to even higher G → T and G → C transversions.

Localization and Expression
Human Neil1 is localized in the centrosomes and in the condensed chromosomes during mitosis. Furthermore, given that there is another protein with overlapping substrate specificity and that Neil1 seems to act very well on bubble substrates, it has been suggested that Neil1 is active during replication and/or transcription.

Medical Implications
8-Oxoguanine can become oxidized to form Sp and Gh and actually show enhanced base misincorporation over the parent 8-oxoG lesion leading to G->T and G->C transversion mutations and thus stall polymerase. Double mouse knockouts of Neil1 and Nth (Nth1(-/-)Neil1(-/-)) show higher incidence of tumors than normal mice. Furthermore, in both mice and humans there is evidence of Neil1 defficiency associated with metabolic syndrome

= Human Neil1 Structure=

Overal Structure
This structure consists of two domains connected by a hinge polypeptide, with an N-terminal domain consisting of a Beta sandwich with two alpha-helices and 4 alpha-helices on the C-terminus , including a H2TH motif and an antiparallel β-hairpin zinc finger motifs.

DNA Binding
Other substrate-bound homologs have many interactions between DNA and protein, including the highly conserved H2TH motif and the zinc finger. Neil1 has both the H2TH motif and a "zincless" finger, an equivalent structural feature that does not bind zinc. . This link has weblogos for the H2TH region

Substrate Recognition
Given its sequence homology, we expect Neil1 to works like other glycosylases, and "flip-out" the damaged base. The actual recognition is still a mystery, but a bacterial homolog (with different substrate specificity) works as follows. An  intercalation loop contains three residues, M77, R112 and F114 which inserts into the space left by the excised base. A recognition complex plays a key role in substrate recognition. Discrimination between a guanine and 8-oxoG might be obtained by the altered protonation state of N7 and an interaction with Ser220.

However, in human Neil1, this recognition complex is absent and a helix takes its place.

Catalysis
The usual mode of catalysis for members of this family starts with a nucleophilic attack from the N-terminal amino group of P2 to the C1' of the damaged base. A schiff base intermediate is formed in the process, and Glu3, Arg258 and Lys57 are involved in the process (<scene name='1tdh/Fpgcatalyticresidues/1' target="fpg">P2,E3,K56 and R242 in Fpg). Several subsequent mechanisms have been proposed. A good illustration can be found in Gilboa et al..

Known Mutations
P2,K56,R248 in E. Coli are known to inactivate the enzyme.

Helix Capping and Pi-Cation Interactions
=References=